Details
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Type:
Epic
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Epic Name:Improve VCF in IGB
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Story Points:0.25
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Sprint:Fall 1, Spring 1, Spring 2, Spring 3, Spring 4, Spring 5, Spring 6, Spring 7, Spring 8, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Fall 2, Fall 3, Fall 4, Fall 5, Fall 6, Fall 7, Fall 8, Fall 9, Spring 1, Spring 2, Spring 3
Description
Link to working VCF folder: https://drive.google.com/drive/folders/1Besca3nbUVhv74l4cW7VSZrgugylngPq?usp=drive_link
Situation: IGB currently has the ability to parse a type of file called VCF (Variant Call Format) which contains information about DNA sequence variants. However, we've encountered user-reported issues in the past of IGB being unable to view VCF files due to their version number and it's been a number of years since we've looked at this parser. We would eventually like to work on a new type of visualization in IGB that involves VCF files, so digging into the codebase and ensuring that IGB can handle VCF files is our first step towards doing so.
Task: Check if there's an updated VCF parser that we can use and, if so, upgrade the VCF parser currently implemented in IGB. See the File Formats page in IGB's smoke-testing documentation for a test VCF file as well as instructions for visualizing that file in IGB: https://wiki.bioviz.org/confluence/display/ITD/File+Formats
To learn more about VCF files, here are some links to documentation and explanatory videos: